niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_surfcluster.py

@@ -0,0 +1,686 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SURFCLUSTER_METADATA = Metadata(
+    id="d511292684dbbb10f74daadd0e2a8026a7360392.boutiques",
+    name="mri_surfcluster",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSurfclusterParameters = typing.TypedDict('MriSurfclusterParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_surfcluster"],
+    "infile": InputPathType,
+    "thmin": typing.NotRequired[float | None],
+    "sign": typing.NotRequired[str | None],
+    "no_adjust_flag": bool,
+    "fdr": typing.NotRequired[float | None],
+    "subject": typing.NotRequired[str | None],
+    "hemi": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+    "surfpath": typing.NotRequired[str | None],
+    "annot": typing.NotRequired[str | None],
+    "frame": typing.NotRequired[float | None],
+    "csd": typing.NotRequired[list[InputPathType] | None],
+    "vwsig": typing.NotRequired[str | None],
+    "cwsig": typing.NotRequired[str | None],
+    "maxcwpval": typing.NotRequired[str | None],
+    "bonferroni": typing.NotRequired[float | None],
+    "sig2p_max_flag": bool,
+    "bonferroni_max": typing.NotRequired[float | None],
+    "csdpdf": typing.NotRequired[str | None],
+    "csdpdf_only_flag": bool,
+    "csd_out": typing.NotRequired[InputPathType | None],
+    "cwpvalthresh": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "fwhmdat": typing.NotRequired[str | None],
+    "clabel": typing.NotRequired[InputPathType | None],
+    "cortex_flag": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_inv_flag": bool,
+    "centroid_flag": bool,
+    "sum": typing.NotRequired[InputPathType | None],
+    "pointset": typing.NotRequired[InputPathType | None],
+    "maxareafile": typing.NotRequired[str | None],
+    "o": typing.NotRequired[str | None],
+    "ocn": typing.NotRequired[str | None],
+    "olab": typing.NotRequired[str | None],
+    "oannot": typing.NotRequired[str | None],
+    "minarea": typing.NotRequired[float | None],
+    "xfm": typing.NotRequired[InputPathType | None],
+    "no_fixmni_flag": bool,
+    "sd": typing.NotRequired[str | None],
+    "thmax": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_surfcluster": mri_surfcluster_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "mri_surfcluster": mri_surfcluster_outputs,
+    }.get(t)
+
+
+class MriSurfclusterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_surfcluster(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface_file: OutputPathType | None
+    """Filtered surface file with non-cluster vertices set to 0"""
+    output_cluster_number_file: OutputPathType | None
+    """Surface file with cluster number per vertex"""
+    output_labels: OutputPathType | None
+    """Label files for clusters"""
+    output_summary_file: OutputPathType | None
+    """Text summary file of clustering results"""
+    output_pointset_file: OutputPathType | None
+    """Pointset file for visualization in Freeview"""
+    output_max_area_file: OutputPathType | None
+    """File containing the area of the largest cluster"""
+
+
+def mri_surfcluster_params(
+    infile: InputPathType,
+    thmin: float | None = None,
+    sign: str | None = None,
+    no_adjust_flag: bool = False,
+    fdr: float | None = None,
+    subject: str | None = None,
+    hemi: str | None = None,
+    surf: str | None = None,
+    surfpath: str | None = None,
+    annot: str | None = None,
+    frame: float | None = None,
+    csd: list[InputPathType] | None = None,
+    vwsig: str | None = None,
+    cwsig: str | None = None,
+    maxcwpval: str | None = None,
+    bonferroni: float | None = None,
+    sig2p_max_flag: bool = False,
+    bonferroni_max: float | None = None,
+    csdpdf: str | None = None,
+    csdpdf_only_flag: bool = False,
+    csd_out: InputPathType | None = None,
+    cwpvalthresh: float | None = None,
+    fwhm: float | None = None,
+    fwhmdat: str | None = None,
+    clabel: InputPathType | None = None,
+    cortex_flag: bool = False,
+    mask: InputPathType | None = None,
+    mask_inv_flag: bool = False,
+    centroid_flag: bool = False,
+    sum_: InputPathType | None = None,
+    pointset: InputPathType | None = None,
+    maxareafile: str | None = None,
+    o: str | None = None,
+    ocn: str | None = None,
+    olab: str | None = None,
+    oannot: str | None = None,
+    minarea: float | None = None,
+    xfm: InputPathType | None = None,
+    no_fixmni_flag: bool = False,
+    sd: str | None = None,
+    thmax: float | None = None,
+) -> MriSurfclusterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Source of surface values.
+        thmin: Minimum intensity threshold.
+        sign: Sign of threshold criteria (abs, pos, neg).
+        no_adjust_flag: Do not adjust threshold for one-tailed tests.
+        fdr: Set thmin with False Discovery Rate.
+        subject: Source surface subject (can be ico).
+        hemi: Cortical hemisphere, either lh or rh.
+        surf: Coordinates from surface (e.g., white).
+        surfpath: Full path to surface.
+        annot: Report annotation for max vertex (e.g., aparc).
+        frame: 0-based frame number of the input file.
+        csd: Load one or more CSD files.
+        vwsig: Map of corrected voxel-wise significances.
+        cwsig: Map of cluster-wise significances.
+        maxcwpval: Save p-value of the largest (max) cluster.
+        bonferroni: Apply Bonferroni correction across N spaces.
+        sig2p_max_flag: Convert max from sig to p.
+        bonferroni_max: Apply Bonferroni correction to maximum.
+        csdpdf: Compute PDF/CDF of CSD data and save.
+        csdpdf_only_flag: Only write the CSD PDF file.
+        csd_out: Write out merged CSD files as one.
+        cwpvalthresh: Cluster-wise threshold.
+        fwhm: FWHM in mm^2 for GRF.
+        fwhmdat: Text file with FWHM in mm^2 for GRF.
+        clabel: Constrain cluster search to be inside or outside clabel.
+        cortex_flag: Set clabel to be subject/label/hemi.cortex.label.
+        mask: Constrain to be within mask.
+        mask_inv_flag: Constrain cluster search to be outside mask or clabel.
+        centroid_flag: Report centroid instead of location of maximum stat.
+        sum_: Text file to store cluster summary.
+        pointset: File that can be read into Freeview with -c.
+        maxareafile: Write area of largest cluster to this file.
+        o: Output file with non-clusters set to 0.
+        ocn: Output file where value is cluster number.
+        olab: Output clusters as labels.
+        oannot: Output clusters as an annotation.
+        minarea: Area threshold for a cluster (mm^2).
+        xfm: Talairach transform file.
+        no_fixmni_flag: Do not fix MNI Talairach coordinates.
+        sd: FreeSurfer subjects directory.
+        thmax: Maximum intensity threshold.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_surfcluster",
+        "infile": infile,
+        "no_adjust_flag": no_adjust_flag,
+        "sig2p_max_flag": sig2p_max_flag,
+        "csdpdf_only_flag": csdpdf_only_flag,
+        "cortex_flag": cortex_flag,
+        "mask_inv_flag": mask_inv_flag,
+        "centroid_flag": centroid_flag,
+        "no_fixmni_flag": no_fixmni_flag,
+    }
+    if thmin is not None:
+        params["thmin"] = thmin
+    if sign is not None:
+        params["sign"] = sign
+    if fdr is not None:
+        params["fdr"] = fdr
+    if subject is not None:
+        params["subject"] = subject
+    if hemi is not None:
+        params["hemi"] = hemi
+    if surf is not None:
+        params["surf"] = surf
+    if surfpath is not None:
+        params["surfpath"] = surfpath
+    if annot is not None:
+        params["annot"] = annot
+    if frame is not None:
+        params["frame"] = frame
+    if csd is not None:
+        params["csd"] = csd
+    if vwsig is not None:
+        params["vwsig"] = vwsig
+    if cwsig is not None:
+        params["cwsig"] = cwsig
+    if maxcwpval is not None:
+        params["maxcwpval"] = maxcwpval
+    if bonferroni is not None:
+        params["bonferroni"] = bonferroni
+    if bonferroni_max is not None:
+        params["bonferroni_max"] = bonferroni_max
+    if csdpdf is not None:
+        params["csdpdf"] = csdpdf
+    if csd_out is not None:
+        params["csd_out"] = csd_out
+    if cwpvalthresh is not None:
+        params["cwpvalthresh"] = cwpvalthresh
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if fwhmdat is not None:
+        params["fwhmdat"] = fwhmdat
+    if clabel is not None:
+        params["clabel"] = clabel
+    if mask is not None:
+        params["mask"] = mask
+    if sum_ is not None:
+        params["sum"] = sum_
+    if pointset is not None:
+        params["pointset"] = pointset
+    if maxareafile is not None:
+        params["maxareafile"] = maxareafile
+    if o is not None:
+        params["o"] = o
+    if ocn is not None:
+        params["ocn"] = ocn
+    if olab is not None:
+        params["olab"] = olab
+    if oannot is not None:
+        params["oannot"] = oannot
+    if minarea is not None:
+        params["minarea"] = minarea
+    if xfm is not None:
+        params["xfm"] = xfm
+    if sd is not None:
+        params["sd"] = sd
+    if thmax is not None:
+        params["thmax"] = thmax
+    return params
+
+
+def mri_surfcluster_cargs(
+    params: MriSurfclusterParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_surfcluster")
+    cargs.extend([
+        "--in",
+        execution.input_file(params.get("infile"))
+    ])
+    if params.get("thmin") is not None:
+        cargs.extend([
+            "--thmin",
+            str(params.get("thmin"))
+        ])
+    if params.get("sign") is not None:
+        cargs.extend([
+            "--sign",
+            params.get("sign")
+        ])
+    if params.get("no_adjust_flag"):
+        cargs.append("--no-adjust")
+    if params.get("fdr") is not None:
+        cargs.extend([
+            "--fdr",
+            str(params.get("fdr"))
+        ])
+    if params.get("subject") is not None:
+        cargs.extend([
+            "--subject",
+            params.get("subject")
+        ])
+    if params.get("hemi") is not None:
+        cargs.extend([
+            "--hemi",
+            params.get("hemi")
+        ])
+    if params.get("surf") is not None:
+        cargs.extend([
+            "--surf",
+            params.get("surf")
+        ])
+    if params.get("surfpath") is not None:
+        cargs.extend([
+            "--surfpath",
+            params.get("surfpath")
+        ])
+    if params.get("annot") is not None:
+        cargs.extend([
+            "--annot",
+            params.get("annot")
+        ])
+    if params.get("frame") is not None:
+        cargs.extend([
+            "--frame",
+            str(params.get("frame"))
+        ])
+    if params.get("csd") is not None:
+        cargs.extend([
+            "--csd",
+            *[execution.input_file(f) for f in params.get("csd")]
+        ])
+    if params.get("vwsig") is not None:
+        cargs.extend([
+            "--vwsig",
+            params.get("vwsig")
+        ])
+    if params.get("cwsig") is not None:
+        cargs.extend([
+            "--cwsig",
+            params.get("cwsig")
+        ])
+    if params.get("maxcwpval") is not None:
+        cargs.extend([
+            "--maxcwpval",
+            params.get("maxcwpval")
+        ])
+    if params.get("bonferroni") is not None:
+        cargs.extend([
+            "--bonferroni",
+            str(params.get("bonferroni"))
+        ])
+    if params.get("sig2p_max_flag"):
+        cargs.append("--sig2p-max")
+    if params.get("bonferroni_max") is not None:
+        cargs.extend([
+            "--bonferroni-max",
+            str(params.get("bonferroni_max"))
+        ])
+    if params.get("csdpdf") is not None:
+        cargs.extend([
+            "--csdpdf",
+            params.get("csdpdf")
+        ])
+    if params.get("csdpdf_only_flag"):
+        cargs.append("--csdpdf-only")
+    if params.get("csd_out") is not None:
+        cargs.extend([
+            "--csd-out",
+            execution.input_file(params.get("csd_out"))
+        ])
+    if params.get("cwpvalthresh") is not None:
+        cargs.extend([
+            "--cwpvalthresh",
+            str(params.get("cwpvalthresh"))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("fwhmdat") is not None:
+        cargs.extend([
+            "--fwhmdat",
+            params.get("fwhmdat")
+        ])
+    if params.get("clabel") is not None:
+        cargs.extend([
+            "--clabel",
+            execution.input_file(params.get("clabel"))
+        ])
+    if params.get("cortex_flag"):
+        cargs.append("--cortex")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_inv_flag"):
+        cargs.append("--mask-inv")
+    if params.get("centroid_flag"):
+        cargs.append("--centroid")
+    if params.get("sum") is not None:
+        cargs.extend([
+            "--sum",
+            execution.input_file(params.get("sum"))
+        ])
+    if params.get("pointset") is not None:
+        cargs.extend([
+            "--pointset",
+            execution.input_file(params.get("pointset"))
+        ])
+    if params.get("maxareafile") is not None:
+        cargs.extend([
+            "--maxareafile",
+            params.get("maxareafile")
+        ])
+    if params.get("o") is not None:
+        cargs.extend([
+            "--o",
+            params.get("o")
+        ])
+    if params.get("ocn") is not None:
+        cargs.extend([
+            "--ocn",
+            params.get("ocn")
+        ])
+    if params.get("olab") is not None:
+        cargs.extend([
+            "--olab",
+            params.get("olab")
+        ])
+    if params.get("oannot") is not None:
+        cargs.extend([
+            "--oannot",
+            params.get("oannot")
+        ])
+    if params.get("minarea") is not None:
+        cargs.extend([
+            "--minarea",
+            str(params.get("minarea"))
+        ])
+    if params.get("xfm") is not None:
+        cargs.extend([
+            "--xfm",
+            execution.input_file(params.get("xfm"))
+        ])
+    if params.get("no_fixmni_flag"):
+        cargs.append("--nofixmni")
+    if params.get("sd") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("sd")
+        ])
+    if params.get("thmax") is not None:
+        cargs.extend([
+            "--thmax",
+            str(params.get("thmax"))
+        ])
+    return cargs
+
+
+def mri_surfcluster_outputs(
+    params: MriSurfclusterParameters,
+    execution: Execution,
+) -> MriSurfclusterOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriSurfclusterOutputs(
+        root=execution.output_file("."),
+        output_surface_file=execution.output_file(params.get("o")) if (params.get("o") is not None) else None,
+        output_cluster_number_file=execution.output_file(params.get("ocn")) if (params.get("ocn") is not None) else None,
+        output_labels=execution.output_file(params.get("olab") + "-*.label") if (params.get("olab") is not None) else None,
+        output_summary_file=execution.output_file(pathlib.Path(params.get("sum")).name) if (params.get("sum") is not None) else None,
+        output_pointset_file=execution.output_file(pathlib.Path(params.get("pointset")).name) if (params.get("pointset") is not None) else None,
+        output_max_area_file=execution.output_file(params.get("maxareafile")) if (params.get("maxareafile") is not None) else None,
+    )
+    return ret
+
+
+def mri_surfcluster_execute(
+    params: MriSurfclusterParameters,
+    execution: Execution,
+) -> MriSurfclusterOutputs:
+    """
+    A tool for clustering vertices on a cortical surface based on intensity values.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSurfclusterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_surfcluster_cargs(params, execution)
+    ret = mri_surfcluster_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_surfcluster(
+    infile: InputPathType,
+    thmin: float | None = None,
+    sign: str | None = None,
+    no_adjust_flag: bool = False,
+    fdr: float | None = None,
+    subject: str | None = None,
+    hemi: str | None = None,
+    surf: str | None = None,
+    surfpath: str | None = None,
+    annot: str | None = None,
+    frame: float | None = None,
+    csd: list[InputPathType] | None = None,
+    vwsig: str | None = None,
+    cwsig: str | None = None,
+    maxcwpval: str | None = None,
+    bonferroni: float | None = None,
+    sig2p_max_flag: bool = False,
+    bonferroni_max: float | None = None,
+    csdpdf: str | None = None,
+    csdpdf_only_flag: bool = False,
+    csd_out: InputPathType | None = None,
+    cwpvalthresh: float | None = None,
+    fwhm: float | None = None,
+    fwhmdat: str | None = None,
+    clabel: InputPathType | None = None,
+    cortex_flag: bool = False,
+    mask: InputPathType | None = None,
+    mask_inv_flag: bool = False,
+    centroid_flag: bool = False,
+    sum_: InputPathType | None = None,
+    pointset: InputPathType | None = None,
+    maxareafile: str | None = None,
+    o: str | None = None,
+    ocn: str | None = None,
+    olab: str | None = None,
+    oannot: str | None = None,
+    minarea: float | None = None,
+    xfm: InputPathType | None = None,
+    no_fixmni_flag: bool = False,
+    sd: str | None = None,
+    thmax: float | None = None,
+    runner: Runner | None = None,
+) -> MriSurfclusterOutputs:
+    """
+    A tool for clustering vertices on a cortical surface based on intensity values.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        infile: Source of surface values.
+        thmin: Minimum intensity threshold.
+        sign: Sign of threshold criteria (abs, pos, neg).
+        no_adjust_flag: Do not adjust threshold for one-tailed tests.
+        fdr: Set thmin with False Discovery Rate.
+        subject: Source surface subject (can be ico).
+        hemi: Cortical hemisphere, either lh or rh.
+        surf: Coordinates from surface (e.g., white).
+        surfpath: Full path to surface.
+        annot: Report annotation for max vertex (e.g., aparc).
+        frame: 0-based frame number of the input file.
+        csd: Load one or more CSD files.
+        vwsig: Map of corrected voxel-wise significances.
+        cwsig: Map of cluster-wise significances.
+        maxcwpval: Save p-value of the largest (max) cluster.
+        bonferroni: Apply Bonferroni correction across N spaces.
+        sig2p_max_flag: Convert max from sig to p.
+        bonferroni_max: Apply Bonferroni correction to maximum.
+        csdpdf: Compute PDF/CDF of CSD data and save.
+        csdpdf_only_flag: Only write the CSD PDF file.
+        csd_out: Write out merged CSD files as one.
+        cwpvalthresh: Cluster-wise threshold.
+        fwhm: FWHM in mm^2 for GRF.
+        fwhmdat: Text file with FWHM in mm^2 for GRF.
+        clabel: Constrain cluster search to be inside or outside clabel.
+        cortex_flag: Set clabel to be subject/label/hemi.cortex.label.
+        mask: Constrain to be within mask.
+        mask_inv_flag: Constrain cluster search to be outside mask or clabel.
+        centroid_flag: Report centroid instead of location of maximum stat.
+        sum_: Text file to store cluster summary.
+        pointset: File that can be read into Freeview with -c.
+        maxareafile: Write area of largest cluster to this file.
+        o: Output file with non-clusters set to 0.
+        ocn: Output file where value is cluster number.
+        olab: Output clusters as labels.
+        oannot: Output clusters as an annotation.
+        minarea: Area threshold for a cluster (mm^2).
+        xfm: Talairach transform file.
+        no_fixmni_flag: Do not fix MNI Talairach coordinates.
+        sd: FreeSurfer subjects directory.
+        thmax: Maximum intensity threshold.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSurfclusterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SURFCLUSTER_METADATA)
+    params = mri_surfcluster_params(
+        infile=infile,
+        thmin=thmin,
+        sign=sign,
+        no_adjust_flag=no_adjust_flag,
+        fdr=fdr,
+        subject=subject,
+        hemi=hemi,
+        surf=surf,
+        surfpath=surfpath,
+        annot=annot,
+        frame=frame,
+        csd=csd,
+        vwsig=vwsig,
+        cwsig=cwsig,
+        maxcwpval=maxcwpval,
+        bonferroni=bonferroni,
+        sig2p_max_flag=sig2p_max_flag,
+        bonferroni_max=bonferroni_max,
+        csdpdf=csdpdf,
+        csdpdf_only_flag=csdpdf_only_flag,
+        csd_out=csd_out,
+        cwpvalthresh=cwpvalthresh,
+        fwhm=fwhm,
+        fwhmdat=fwhmdat,
+        clabel=clabel,
+        cortex_flag=cortex_flag,
+        mask=mask,
+        mask_inv_flag=mask_inv_flag,
+        centroid_flag=centroid_flag,
+        sum_=sum_,
+        pointset=pointset,
+        maxareafile=maxareafile,
+        o=o,
+        ocn=ocn,
+        olab=olab,
+        oannot=oannot,
+        minarea=minarea,
+        xfm=xfm,
+        no_fixmni_flag=no_fixmni_flag,
+        sd=sd,
+        thmax=thmax,
+    )
+    return mri_surfcluster_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SURFCLUSTER_METADATA",
+    "MriSurfclusterOutputs",
+    "MriSurfclusterParameters",
+    "mri_surfcluster",
+    "mri_surfcluster_params",
+]